NetChop 3.1.ws1

Prediction of proteasomal cleavages (MHC ligands)

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Documentation

INTRODUCTION
This Web Service implements NetChop v. 3.1.ws0. It produces neural network
predictions for cleavage sites of the human proteasome. The method is
described in detail in the following article:
The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M Nielsen, C Lundegaard, O Lund, and C Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.
Alongside this Web Service the NetChop method is also implemented as
a traditional click-and-paste WWW server at:
http://www.cbs.dtu.dk/services/NetChop/
NetChop is also available as a stand-alone software package to install
and run at the user's site, with the same functionality. For academic
users there is a download page at:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop
Other users are requested to write to software@cbs.dtu.dk for details.
WEB SERVICE OPERATION
This Web Service is fully asynchronous; the usage is split into the
following three operations:
1. runService
Input: The following parameters and data:
* 'method' prediction method:
0 for "C term 3.0", 1 for "20S 3.0";
* 'threshold' threshold for yes/no decision.
The default is 0.5; increasing the threshold results in better
specificity, but worse sensitivity;
* 'sequencedata' mulitple elements of type 'sequence':
* 'sequence' answers to one sequence:
* 'id' unique identifier for the sequence;
* 'comment' optional comment;
* 'seq' protein sequence. The sequence must be written
using the one letter amino acid code:
`acdefghiklmnpqrstvwy' or `ACDEFGHIKLMNPQRSTVWY'.
Other letters will be converted to `X' and treated
as unknown amino acids. Other symbols,
such as whitespace and numbers, will be ignored.
Output: Unique job identifier
2. pollQueue
Input: Unique job identifier
Output: 'jobstatus' - the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN
3. fetchResult
Input: Unique job identifier of a finished job
Output: * 'annsource'
'method' name of the method, here always 'NetChop';
'version' version of the method: here always '3.1 ws0';
'ann' annotations - one element per input sequence;
'sequence' standard sequence object;
'id' sequence identifier;
'annrecords/annrecord'
'feature' feature name, here always 'NetChop';
'pos' always present, indicates the position in the sequence;
'score'
'key' score key name, here always 'main', indicating the main prediction score;
'value' prediction score value;
'comment' gives 'S' for identified cleavage sites. Appears only if the prediction score
is greater than the threshold.
CONTACT
Questions concerning the scientific aspects of the NetChop method should go
to Morten Nielsen, mniel@cbs.dtu.dk; technical question concerning the Web
Service should go to Karunakar Bayyapu, karun@cbs.dtu.dk or Kristoffer
Rapacki, rapacki@cbs.dtu.dk.